The dataset contains all the underpinning data for the manuscript entitled "High resolution magnetic microscopy based on semi-encapsulated graphene Hall sensors" published in Applied Physics Letters. This includes the characterisation data for semi-encapsulated nanoscale graphene Hall sensors as well as the results of their use to image ferrimagnetic domains in a Yttrium Iron Garnet (YIG) film. The manuscript describes the 'hot pick-up' protocol used to fabricate sensors as well as characterisation of the key figures-of merit, i.e., sensitivity and minimum detectable field. The improvement in quality due to partial encapsulation quality is demonstrated and proof-of-principle measurements made of ferrimagnetic domains in a YIG film under applied in-plane magnetic fields.